|
| Status |
Public on Jun 01, 2010 |
| Title |
tomato Moneymaker unstressed 5 h rep3. |
| Sample type |
RNA |
| |
|
| Source name |
Moneymaker, unstressed, 5 h
|
| Organism |
Solanum lycopersicum |
| Characteristics |
genotype: Moneymaker
age of plant: 6-leaf-old
tissue: whole plant
treatment: unstress
treatment time: 5 h.
|
| Biomaterial provider |
Tomato Genetics Resource Center
|
| Treatment protocol |
For salt treatment, 4-week-old plants were transferred to aerated hydroponic tanks containing 1/4- strength Hoagland solution in a greenhouse. After acclimating for 3 d, tomato plants having six true leaves were treated with fresh 1/4-strength Hoagland solution with 0 mM NaCl.
|
| Growth protocol |
Seeds of uniform size were surface-sterilized by soaking in 70% (v/v) ethanol for 2 min, then in 2.63% (w/v) NaOC1 for 30 min, and finally rinsed five times with sterile distilled water. The seeds were sown in petri dish containing 10 ml of double distilled H2O and germinated under 16 hr light (1500 lux) at 26℃ in a growth chamber. 7 d later, seedlings were planted in pots containing sterile sand supplemented with 1/4-strength Hoagland solution in a greenhouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
In one treatment, 9 six-leaf-old tomato plants were divided into three biological replicates and treated hydroponically under sterile condition with 0 mM NaCl for 5 h. RNA isolated from pooled three individual plants was used in hybridization to one chip.
Total RNA was isolated using a hot phenol method (Kay et al., 1987).
|
| Label |
biotin
|
| Label protocol |
10 μg total RNA was first reverse transcribed using a T7-Oligo (dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
|
| |
|
| Hybridization protocol |
The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip® Tomato Genome Arrays according to the protocols provided by the manufacturer. Immediately following hybridization, the probe array underwent an automated washing and staining protocol on the fluidics station 450.
|
| Scan protocol |
Then arrays were scanned with Affymetrix® GeneChip® Scanner 3000, and the resulting images were analyzed with Affymetrix® GeneChip® Operating Software (GCOS 1.4).
|
| Description |
6-leaf-old whole plant of Moneymaker, unstressed for 5 h as a control.
|
| Data processing |
A dChip normalization method was employed to normalize the ratio values. Normalized ratio data were then log transformed. Differentially expressed genes were identified using SAM software and multiple test corrections were performed using False Discovery Rate (FDR).
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| |
|
| Submission date |
Jun 03, 2009 |
| Last update date |
Jun 01, 2010 |
| Contact name |
Wei Sun |
| E-mail(s) |
sunweicaas@tom.com, sunweicaas@hotmail.com
|
| Organization name |
Institute of Botany, Chinese Academy of Sciences
|
| Street address |
20 Nan Xin Cun
|
| City |
Beijing |
| ZIP/Postal code |
100093 |
| Country |
China |
| |
|
| Platform ID |
GPL4741 |
| Series (1) |
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